Properties of Chaperones:

Which statement about Chaperones is true?

A) Most proteins need the assistance of Chaperones to fold

inside the cell.
B) Some proteins are folded only by HSP-60 and do not need
HSP-70
C) HSP-70 binds to proteins as they are being synthesized by
the ribosome
D) HSP-60 binds to proteins after they have been completely
synthesized
 Properties of Chaperones:

How do Chaperones recognize proteins that are NOT

completely folded? (so they can bind to those proteins to
help them fold)
A) Chaperones can recognize the shape of unfolded proteins.
B) Chaperones can recognize the shape of folded proteins.
C) Chaperones bind to patches of hydrophobic amino acids
on other proteins.
D) Chaperones bind to patches of hydrophilic amino acids on
other proteins.
E) Chaperones bind equally well to a folded or unfolded
protein.
 Ubiquitylation

Which of the following proteins determines which protein lives or dies by

ubiquitin-mediated degradation?

A) HSP-70
B) Ubiquitin Activating Enzyme
C) E2
D) E3
E) Proteasome core
 Experimental Question:
You have a drug that blocks the activity of one of the
enzymes involved in ubiquitylation of proteins. You treat cells
with this drug and you determine the effect of treatment on
the abundance of different proteins by Western blot analysis.
Cdc2 is a control of a protein that is not ubiquitylated. From
the literature you know that the other 4 proteins are
ubiquitylated by different E2+E3 ligase proteins.

Based on this information you can conclude that:

A = The drug blocks the activity of Ubiquitin Activating Enzyme (E1)

B = The drug blocks the activity of a Ubiquitin E2 protein
C = The drug blocks the activity of a Ubiquitin E3 protein
D = Protein synthesis is increased by the drug treatment
 Experimental Question:
You have a drug that blocks the activity of the Proteasome. You treat cells
with this drug and you determine the effect of treatment on the abundance
of your favorite protein by Western blot analysis.

The arrow points to the size of your favorite protein (YFP).

Blot probed with anti-YFP

antibodies

YFP

0 6 12 hours
Based on this Western blot you can conclude that:
A = proteins larger than YFP are synthesized
B = drug treatment does not affect YFP in any way
C = drug treatment causes YFP to be destroyed in the proteasome
D = drug treatment causes YFP to become ubiquitylated
E = drug treatment caused the accumulation of ubiquitylated-YFP
 Experimental Question:
How can you show that the bands larger than YFP represent
polyubiquitylated forms of YFP?

YFP

0 6 12 hours

Blot probed with anti-YFP

antibodies
Stable β-sheet aggregates can form from many proteins, forming intertwined
cross-beta strands that have the potential to kill cells or damage tissues.
Which of the following is NOT true regarding these aggregates?

A. They form almost exclusively in the cells of the nervous system.

B. Different types of such aggregates can form from the same protein.

C. Their formation is associated with conditions such as Parkinson’s disease

and Kuru.

D. They can form spontaneously, but also can be triggered to form by an

infection with the same aggregate.

E. Some healthy cells form these aggregates to store their secretory proteins.
 Lecture 3 DNA, chromosome and Genome-

• Gene:
• Double strand (how to read)
• DNA duplication
• How to improve DNA is heritable?
• Chromatin:
• Histone
• Histone modification
• Human genome
discovered in 1953 by Watson and Crick at the University of Cambridge
, sing experimental data collected by Rosalind Franklin and
Maurice Wilkins. The structure of DNA is non-static,[9]
all species comprises two helical chains each coiled round the same axi
s, and each with a pitch of 34
Adenine Thymine

Guanine Cytosine
purine pyrimidine
• Indicate which numbered feature (1 to 5) in the schematic
drawing below of the DNA double helix corresponds to each
of the following. Your answer would be a five-digit number
composed of digits 1 to 5 only, e.g. 52431.

( ) Hydrogen-bonding
( ) Covalent linkage
( ) Phosphate group
( ) Nitrogen-containing base
( ) Deoxyribose sugar
• Indicate which numbered feature (1 to 5) in the schematic
drawing below of the DNA double helix corresponds to each
of the following. Your answer would be a five-digit number
composed of digits 1 to 5 only, e.g. 52431.

(4) Hydrogen-bonding
(3) Covalent linkage
(2) Phosphate group
(1) Nitrogen-containing base
(5) Deoxyribose sugar
THE STRUCTURE AND FUNCTION
OF DNA
In living organisms DNA does not usually exist as a single molecule, but instead as
a pair of molecules that are held tightly together
 The Structure of DNA Provides a Mechanism
for Heredity

1. semi conservative
2. 5’-3’ synthesis
3. 3’-5’ proofreading
DNA polymerases have
proofreading abilities.
 Chromosomal DNA and Its Packaging in the
Chromatin Fiber

Each chromosome in a eukaryotic cell consists of a single, enormously long linear

DNA molecule along with the proteins that fold and pack the fine DNA thread into
a more compact structure.

The complex of DNA and tightly bound protein is called chromatin

 Human cell nucleus
Each human cell nucleus contains two copies of each
chromosome, one inherited from the mother and one
from the father.
The maternal and paternal chromosomes of a pair are
called homologous chromosomes(homologs ).

The only nonhomologous chromosome pairs are the sex

chromosomesin males, where a Y chromosome is
inherited from the father and an X chromosome from the
mother.
The human genome is
how little of it (only a few
percent) codes for
proteins, about 1.5%.
These exons constitute
roughly 6% of our genes

large average gene

size—about 27,000 bp

Only about 5% of our

genome is highly
conserved.

About 50% of our genome

is made of various
repeated sequences, most
notably the transposable
DNA elements.
Craig Venter

Funder of celera genomics, the institute of

genomic research and JCVI (create
synthetic biological organisms)

Venter himself recognized his own

ADHD behavior in his adolescence, and la
ter found ADHD-linked genes in his own D
NA
• Chromosome 3 contains nearly 200 million
nucleotide pairs of our genome. If this DNA
molecule could be laid end to end, how long
would it be? The distance between neighboring
base pairs in DNA is typically around 0.34 nm.
• A. About 7 mm
• B. About 7 cm
• C. About 70 cm
• D. About 7 m
• E. None of the above
 Nucleosomes Are a
Basic Unit of Eukaryotic
Chromosome
Structure
The structure of a nucleosome core particle, as determined by x-ray diffraction
analyses of crystals. Each histone is colored according to the scheme in Figure 4–22,
with the DNA double helix in light gray. (Adapted from K. Luger et al., Nature 389:251–260,
1997. With permission from Macmillan Publishers Ltd.)
• Indicate which feature (1 to 4) in the schematic drawing
below of a chromatin fiber corresponds to each of the
following. Your answer would be a four-digit number
composed of digits 1 to 4 only, e.g. 2431.
•

• ( ) Nucleosome core particle

• ( ) Linker DNA
• ( ) Histone octamer
• ( ) Non-histone protein
Schematic diagram showing
how a particular combination of
histone modifications can be
recognized by a reader complex. A
large protein complex that contains a
series of protein modules, each of
which recognizes a specific histone
mark, is schematically illustrated
(green). This “reader complex” will
bind tightly only to a region of
chromatin that contains several of the
different histone marks that it
recognizes. Therefore, only a specific
combination of marks will cause the
complex to bind to chromatin and
attract the additional protein
complexes (purple) needed to catalyze
a biological function.
 You have begun to characterize a sample obtained
from the depths of the oceans on Europa, one of Jupiter’s
moons. Much to your surprise, the sample contains
a life-form that grows well in a rich broth. Your preliminary
analysis shows that it is cellular and contains DNA,
RNA, and protein. When you show your results to a colleague,
she suggests that your sample was contaminated
with an organism from Earth. What approaches might
you try to distinguish between contamination and a
novel cellular life-form based on DNA, RNA, and protein?
Stable β-sheet aggregates can form from many proteins, forming intertwined
cross-beta strands that have the potential to kill cells or damage tissues.
Which of the following is NOT true regarding these aggregates?

A. They form almost exclusively in the cells of the nervous system.

B. Different types of such aggregates can form from the same protein.

C. Their formation is associated with conditions such as Parkinson’s disease

and Kuru.

D. They can form spontaneously, but also can be triggered to form by an

infection with the same aggregate.

E. Some healthy cells form these aggregates to store their secretory proteins.